NASA's Europa Clipper Launch

Nope. They needed the maximum amount of thrust from those boosters in order to propel the spacecraft toward Jupiter, so they couldn't save enough fuel for the boosters to land themselves. This was the 6th flight of these boosters, so we thank them for their service!

Is this one of those things that’s limited by physics or at some point will these kinds of missions be doable with a mostly reusable setup?

It's the tyranny of the rocket equation. The more you send up, the more fuel you need to send up and then you need to send fuel to lift that fuel and then fuel to lift that fuel and so on.

Since you have to have a burn to slow down and land you have to carry extra fuel to recover. That's always going to be the case, but starship is making strides towards minimizing that as much as possible with belly flops and chopsticks

It's a limitation of the Falcon Heavy, the launcher used this time. A future, more powerful one could do it while being reusable.

It's limited by physics: if a reusable rocket can carry a maximum payload of X tons, it can only be reused when it carries a payload of X/N tons, and (1-X)/N as extra fuel. How large X and N are of course depends on the rocket design, but N is always going to be greater than 1.

So, for any rocket, flying it reusably is going to mean not using the full capacity.

Sure, a bigger rocket could carry this particular payload while being reusable. But for any rocket there will always be payloads it can't carry while also having enough fuel to land.

It's an engineering tradeoff of payload vs. booster cost. It's heavily one-sided for this launch—you get 4x more payload to this interplanetary orbit with the expendable Heavy vs. the reusable one [a].

Future launches with Starship, analogous to this one, would refuel their upper stage in orbit to their full capacity, so there would be no performance downside to recovering boosters; you would need more launches, but they would all be reusable.

[a] https://elvperf.ksc.nasa.gov/Pages/Query.aspx (I queried for a high-energy orbit with a C3 of 42 km^2/s^2, which I think is correct, or at least very close)

It's limited by physics: Recovering the rockets requires counteracting gravity, which requires energy. If the energy is needed for something else - in this case for additional propulsion - then it's not available for recovery.

They traded off the expense of expending a whole Falcon Heavy against the benefit of having additional delta-V to get to Jupiter faster.

That constraint can be significantly mitigated by in-space refueling. Then it just becomes a matter of what the rocket can lift into a stable orbit.

Edit: Not that this applies to any currently operational rockets.

Also with starship launches only needing about a million dollars in fuel, it makes a ton of sense to just launch fuel to orbit versus sacrificing an entire ship

You could build a larger re-usable rocket that could launch this payload and still have margin for recovery, such as the in-development SpaceX Starship.

However for this type of mission that would still leave the question of "What if we skipped re-usability and paid more to expend the launcher? Could we launch a larger payload and/or get there faster?"

The trajectory for this mission was already a slower transit time than the alternate plan of launching it on the SLS rocket. I think for some missions that are infrequent and targeting far-away destinations there will always be a desire to maximize performance at the cost of reusability on that singular launch.

You just go to distributed launch. You launch a rocket multiple times, fuel up and use that to escape. If you use your upper stage as the primary, its unlikely to ever come back.

But in future you would potentially have special boost stage for that. See something like Impulse Space is building.

But for these really powerful throws, its probably just cheaper to just drop an upper stage. Upper stages are a drop in the bucket compared to the cost of a flagship mission. A Falcon 9 upper stage is only a couple million $.